They'll get punched out with little difficulty when you decap. If you're already decapped, I've not known too many folks to decap before tumbling, but if that's what you're doing, then run them through the decap station again (or decapper if you're doing it by hand). I don't know any other way.
I just went to ultrasonic and it does solve the problem--and the problem of having polishing rouge all over the brass--and the problem of not having clean primer pockets or clean case interiors.
This is your typical filthy brass with black primer pockets and black interiors, after 8 minutes in a $75 Harbor Freight ultrasonic tank. Rinsed in hot water and blown off with a hot air gun. No dust, particles, rouge and no need for further polish. I did 1,000 case one evening while reloading.